2-127000872-C-T

Variant names:

• chr2-127000872-C-T
• rs12993006

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.278 in 152,120 control chromosomes in the GnomAD database, including 7,360 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42236 AN: 152002 Hom.: 7341 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.220

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.278 AC: 42299 AN: 152120 Hom.: 7360 Cov.: 32 AF XY: 0.270 AC XY: 20080 AN XY: 74378

African (AFR) AF: 0.475 AC: 19684 AN: 41468

American (AMR) AF: 0.156 AC: 2382 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3466

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5186

South Asian (SAS) AF: 0.0702 AC: 339 AN: 4828

European-Finnish (FIN) AF: 0.228 AC: 2410 AN: 10568

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16294 AN: 67986

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.232 Hom.: 14647

Bravo AF: 0.278

Asia WGS AF: 0.0730 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.23
PhyloP100		-0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12993006; hg19: chr2-127758448;